[English] 日本語
Yorodumi- PDB-1lst: THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-, ARGININE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lst | ||||||
---|---|---|---|---|---|---|---|
Title | THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN WITH AND WITHOUT A LIGAND | ||||||
Components | LYSINE, ARGININE, ORNITHINE-BINDING PROTEIN | ||||||
Keywords | AMINO-ACID BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Kim, S.-H. / Oh, B.-H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand. Authors: Oh, B.H. / Pandit, J. / Kang, C.H. / Nikaido, K. / Gokcen, S. / Ames, G.F. / Kim, S.H. #1: Journal: J.Biol.Chem. / Year: 1992 Title: Crystal Structure of the Lysine-, Arginine-, Ornithine-Binding Protein from Salmonella Typhimurium at 2.7 Angstroms Resolution Authors: Kang, C.-H. / Shin, W.-C. / Yamagata, Y. / Gokcen, S. / Ames, G.F.-L. / Kim, S.-H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lst.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lst.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/1lst ftp://data.pdbj.org/pub/pdb/validation_reports/ls/1lst | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO 16 |
-Components
#1: Protein | Mass: 26187.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P02911 |
---|---|
#2: Chemical | ChemComp-LYS / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.67 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 23359 / % possible obs: 93 % / Observed criterion σ(F): 1 / Num. measured all: 92644 / Rmerge(I) obs: 0.0405 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→6 Å / σ(F): 1 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.165 / Rfactor Rwork: 0.165 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|